FMO DATABASE

FMODB ID: NN7GQ

Calculation Name: 2C0L-B-Xray372

Preferred Name: Non-specific lipid-transfer protein

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2C0L

Chain ID: B

ChEMBL ID: CHEMBL5950

UniProt ID: P22307

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	122
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-972111.993982
FMO2-HF: Nuclear repulsion	925457.659665
FMO2-HF: Total energy	-46654.334317
FMO2-MP2: Total energy	-46788.261647

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(B:22:SER)

Summations of interaction energy for fragment #1(B:22:SER)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-23.258	-17.673	6.982	-6.544	-6.023	-0.056

Interaction energy analysis for fragmet #1(B:22:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.037 / q_NPA : -0.023

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

Sort

Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	B	24	SER	0	0.033	0.017	3.765	-0.756	0.814	0.003	-0.630	-0.943	0.002
4	B	25	ASP	-1	-0.861	-0.929	2.139	-24.904	-21.352	6.970	-5.718	-4.804	-0.059
5	B	26	GLY	0	-0.020	-0.010	4.042	1.440	1.480	-0.001	-0.018	-0.021	0.000
6	B	27	PHE	0	-0.069	-0.030	7.053	0.524	0.524	0.000	0.000	0.000	0.000
7	B	28	LYS	1	0.925	0.948	9.260	0.330	0.330	0.000	0.000	0.000	0.000
8	B	29	ALA	0	0.027	0.011	11.291	-0.010	-0.010	0.000	0.000	0.000	0.000
9	B	30	ASN	0	0.011	0.005	6.195	0.504	0.504	0.000	0.000	0.000	0.000
10	B	31	LEU	0	-0.038	-0.014	9.425	-0.005	-0.005	0.000	0.000	0.000	0.000
11	B	32	VAL	0	0.015	0.014	12.216	0.066	0.066	0.000	0.000	0.000	0.000
12	B	33	PHE	0	0.007	-0.015	10.640	0.072	0.072	0.000	0.000	0.000	0.000
13	B	34	LYS	1	0.984	1.001	6.923	1.975	1.975	0.000	0.000	0.000	0.000
14	B	35	GLU	-1	-0.925	-0.961	12.161	-0.335	-0.335	0.000	0.000	0.000	0.000
15	B	36	ILE	0	-0.092	-0.039	15.254	0.046	0.046	0.000	0.000	0.000	0.000
16	B	37	GLU	-1	-0.918	-0.990	11.051	-0.393	-0.393	0.000	0.000	0.000	0.000
17	B	38	LYS	1	0.921	0.976	13.794	0.549	0.549	0.000	0.000	0.000	0.000
18	B	39	LYS	1	0.980	0.996	17.327	0.212	0.212	0.000	0.000	0.000	0.000
19	B	40	LEU	0	-0.082	-0.043	17.212	0.026	0.026	0.000	0.000	0.000	0.000
20	B	41	GLU	-1	-0.900	-0.958	17.506	-0.102	-0.102	0.000	0.000	0.000	0.000
21	B	42	GLU	-1	-0.979	-0.960	19.953	-0.187	-0.187	0.000	0.000	0.000	0.000
22	B	43	GLU	-1	-1.000	-1.007	23.136	-0.098	-0.098	0.000	0.000	0.000	0.000
23	B	44	GLY	0	0.065	0.028	22.496	0.009	0.009	0.000	0.000	0.000	0.000
24	B	45	GLU	-1	-0.984	-1.005	23.125	-0.023	-0.023	0.000	0.000	0.000	0.000
25	B	46	GLN	0	-0.007	-0.008	26.391	0.011	0.011	0.000	0.000	0.000	0.000
26	B	47	PHE	0	-0.024	-0.019	23.638	0.008	0.008	0.000	0.000	0.000	0.000
27	B	48	VAL	0	-0.012	0.016	23.529	0.007	0.007	0.000	0.000	0.000	0.000
28	B	49	LYS	1	0.914	0.964	25.897	0.029	0.029	0.000	0.000	0.000	0.000
29	B	50	LYS	1	0.918	0.967	28.360	0.064	0.064	0.000	0.000	0.000	0.000
30	B	51	ILE	0	-0.043	-0.003	23.574	0.003	0.003	0.000	0.000	0.000	0.000
31	B	52	GLY	0	0.076	0.054	26.383	0.004	0.004	0.000	0.000	0.000	0.000
32	B	53	GLY	0	-0.016	-0.018	24.926	0.006	0.006	0.000	0.000	0.000	0.000
33	B	54	ILE	0	-0.082	-0.006	19.196	-0.001	-0.001	0.000	0.000	0.000	0.000
34	B	55	PHE	0	0.028	0.005	18.465	-0.004	-0.004	0.000	0.000	0.000	0.000
35	B	56	ALA	0	0.056	0.031	16.239	0.024	0.024	0.000	0.000	0.000	0.000
36	B	57	PHE	0	-0.014	-0.023	13.857	-0.041	-0.041	0.000	0.000	0.000	0.000
37	B	58	LYS	1	0.969	0.979	13.728	-0.130	-0.130	0.000	0.000	0.000	0.000
38	B	59	VAL	0	0.003	0.009	12.243	-0.025	-0.025	0.000	0.000	0.000	0.000
39	B	60	LYS	1	0.949	0.972	12.996	-0.092	-0.092	0.000	0.000	0.000	0.000
40	B	61	ASP	-1	-0.889	-0.951	15.269	-0.029	-0.029	0.000	0.000	0.000	0.000
41	B	62	GLY	0	0.034	0.019	11.534	-0.046	-0.046	0.000	0.000	0.000	0.000
42	B	63	PRO	0	-0.026	-0.017	8.699	0.093	0.093	0.000	0.000	0.000	0.000
43	B	64	GLY	0	-0.012	-0.012	10.597	0.090	0.090	0.000	0.000	0.000	0.000
44	B	65	GLY	0	0.018	0.018	12.820	0.050	0.050	0.000	0.000	0.000	0.000
45	B	66	LYS	1	0.867	0.944	6.077	-0.280	-0.280	0.000	0.000	0.000	0.000
46	B	67	GLU	-1	-0.892	-0.964	10.598	0.145	0.145	0.000	0.000	0.000	0.000
47	B	68	ALA	0	-0.023	0.007	7.937	0.067	0.067	0.000	0.000	0.000	0.000
48	B	69	THR	0	-0.003	-0.013	8.672	-0.097	-0.097	0.000	0.000	0.000	0.000
49	B	70	TRP	0	0.016	0.016	7.567	0.221	0.221	0.000	0.000	0.000	0.000
50	B	71	VAL	0	0.006	0.003	11.379	-0.055	-0.055	0.000	0.000	0.000	0.000
51	B	72	VAL	0	0.009	0.014	14.121	0.002	0.002	0.000	0.000	0.000	0.000
52	B	73	ASP	-1	-0.853	-0.958	16.375	0.071	0.071	0.000	0.000	0.000	0.000
53	B	74	VAL	0	0.084	0.038	18.754	-0.016	-0.016	0.000	0.000	0.000	0.000
54	B	75	LYS	1	0.871	0.947	21.721	-0.070	-0.070	0.000	0.000	0.000	0.000
55	B	76	ASN	0	-0.022	-0.017	21.734	-0.010	-0.010	0.000	0.000	0.000	0.000
56	B	77	GLY	0	0.035	0.012	22.552	-0.002	-0.002	0.000	0.000	0.000	0.000
57	B	78	LYS	1	0.927	0.958	21.695	0.051	0.051	0.000	0.000	0.000	0.000
58	B	79	GLY	0	0.060	0.045	20.090	-0.016	-0.016	0.000	0.000	0.000	0.000
59	B	80	SER	0	-0.068	-0.043	15.257	0.004	0.004	0.000	0.000	0.000	0.000
60	B	81	VAL	0	0.030	0.016	11.068	0.003	0.003	0.000	0.000	0.000	0.000
61	B	82	LEU	0	-0.048	-0.022	10.938	0.027	0.027	0.000	0.000	0.000	0.000
62	B	83	PRO	0	0.022	-0.011	6.015	-0.058	-0.058	0.000	0.000	0.000	0.000
63	B	84	ASN	0	-0.014	-0.015	3.604	-1.997	-1.574	0.010	-0.178	-0.255	0.001
64	B	85	SER	0	-0.011	0.013	7.494	-0.054	-0.054	0.000	0.000	0.000	0.000
65	B	86	ASP	-1	-0.924	-0.957	10.861	0.383	0.383	0.000	0.000	0.000	0.000
66	B	87	LYS	1	0.944	0.975	13.702	-0.203	-0.203	0.000	0.000	0.000	0.000
67	B	88	LYS	1	0.929	0.961	16.534	-0.143	-0.143	0.000	0.000	0.000	0.000
68	B	89	ALA	0	0.020	-0.003	19.198	-0.001	-0.001	0.000	0.000	0.000	0.000
69	B	90	ASP	-1	-0.850	-0.920	21.242	0.058	0.058	0.000	0.000	0.000	0.000
70	B	91	CYS	0	-0.084	-0.026	22.556	-0.011	-0.011	0.000	0.000	0.000	0.000
71	B	92	THR	0	-0.018	-0.005	18.810	0.021	0.021	0.000	0.000	0.000	0.000
72	B	93	ILE	0	0.017	0.011	18.722	-0.014	-0.014	0.000	0.000	0.000	0.000
73	B	94	THR	0	-0.030	-0.007	18.009	0.019	0.019	0.000	0.000	0.000	0.000
74	B	95	MET	0	-0.014	0.000	17.862	-0.009	-0.009	0.000	0.000	0.000	0.000
75	B	96	ALA	0	0.095	0.069	17.243	0.003	0.003	0.000	0.000	0.000	0.000
76	B	97	ASP	-1	-0.706	-0.884	12.721	-0.441	-0.441	0.000	0.000	0.000	0.000
77	B	98	SER	0	-0.001	-0.012	15.307	-0.022	-0.022	0.000	0.000	0.000	0.000
78	B	99	ASP	-1	-0.881	-0.947	17.855	-0.075	-0.075	0.000	0.000	0.000	0.000
79	B	100	PHE	0	-0.008	-0.012	14.618	0.007	0.007	0.000	0.000	0.000	0.000
80	B	101	LEU	0	0.022	0.014	16.024	-0.007	-0.007	0.000	0.000	0.000	0.000
81	B	102	ALA	0	0.005	0.032	18.109	0.005	0.005	0.000	0.000	0.000	0.000
82	B	103	LEU	0	-0.043	-0.031	21.123	0.009	0.009	0.000	0.000	0.000	0.000
83	B	104	MET	0	0.003	0.007	17.972	0.014	0.014	0.000	0.000	0.000	0.000
84	B	105	THR	0	-0.059	-0.060	19.563	-0.009	-0.009	0.000	0.000	0.000	0.000
85	B	106	GLY	0	0.019	0.010	22.143	0.004	0.004	0.000	0.000	0.000	0.000
86	B	107	LYS	1	0.858	0.939	24.030	0.150	0.150	0.000	0.000	0.000	0.000
87	B	108	MET	0	-0.045	-0.019	23.637	0.017	0.017	0.000	0.000	0.000	0.000
88	B	109	ASN	0	0.061	0.049	26.465	-0.012	-0.012	0.000	0.000	0.000	0.000
89	B	110	PRO	0	0.058	0.023	25.355	0.002	0.002	0.000	0.000	0.000	0.000
90	B	111	GLN	0	0.074	0.016	26.782	0.002	0.002	0.000	0.000	0.000	0.000
91	B	112	SER	0	0.024	0.010	29.665	0.003	0.003	0.000	0.000	0.000	0.000
92	B	113	ALA	0	-0.006	0.001	25.129	0.004	0.004	0.000	0.000	0.000	0.000
93	B	114	PHE	0	-0.023	-0.008	27.280	0.005	0.005	0.000	0.000	0.000	0.000
94	B	115	PHE	0	-0.005	-0.008	28.431	0.005	0.005	0.000	0.000	0.000	0.000
95	B	116	GLN	0	-0.037	-0.024	28.507	0.000	0.000	0.000	0.000	0.000	0.000
96	B	117	GLY	0	-0.016	0.007	28.649	0.001	0.001	0.000	0.000	0.000	0.000
97	B	118	LYS	1	0.893	0.951	24.129	0.062	0.062	0.000	0.000	0.000	0.000
98	B	119	LEU	0	-0.029	-0.002	21.989	-0.003	-0.003	0.000	0.000	0.000	0.000
99	B	120	LYS	1	0.941	0.971	22.753	-0.021	-0.021	0.000	0.000	0.000	0.000
100	B	121	ILE	0	0.032	0.001	22.788	0.003	0.003	0.000	0.000	0.000	0.000
101	B	122	THR	0	-0.029	-0.004	23.629	0.002	0.002	0.000	0.000	0.000	0.000
102	B	123	GLY	0	0.058	0.025	24.993	0.002	0.002	0.000	0.000	0.000	0.000
103	B	124	ASN	0	0.023	0.001	27.057	-0.011	-0.011	0.000	0.000	0.000	0.000
104	B	125	MET	0	0.075	0.031	27.187	-0.004	-0.004	0.000	0.000	0.000	0.000
105	B	126	GLY	0	0.022	0.011	28.957	-0.006	-0.006	0.000	0.000	0.000	0.000
106	B	127	LEU	0	-0.046	-0.026	23.802	-0.007	-0.007	0.000	0.000	0.000	0.000
107	B	128	ALA	0	0.073	0.019	24.344	-0.007	-0.007	0.000	0.000	0.000	0.000
108	B	129	MET	0	-0.042	-0.010	25.215	-0.012	-0.012	0.000	0.000	0.000	0.000
109	B	130	LYS	1	0.847	0.920	26.565	-0.002	-0.002	0.000	0.000	0.000	0.000
110	B	131	LEU	0	0.026	0.020	19.826	-0.005	-0.005	0.000	0.000	0.000	0.000
111	B	132	GLN	0	-0.001	-0.023	23.139	-0.020	-0.020	0.000	0.000	0.000	0.000
112	B	133	ASN	0	-0.051	-0.033	25.309	0.000	0.000	0.000	0.000	0.000	0.000
113	B	134	LEU	0	0.010	0.004	19.095	-0.005	-0.005	0.000	0.000	0.000	0.000
114	B	135	GLN	0	-0.038	0.008	20.800	-0.014	-0.014	0.000	0.000	0.000	0.000
115	B	136	LEU	0	-0.011	0.006	17.235	-0.001	-0.001	0.000	0.000	0.000	0.000
116	B	137	GLN	0	-0.035	-0.033	21.896	0.015	0.015	0.000	0.000	0.000	0.000
117	B	138	PRO	0	-0.008	0.017	25.034	-0.006	-0.006	0.000	0.000	0.000	0.000
118	B	139	GLY	0	0.038	0.022	26.954	0.010	0.010	0.000	0.000	0.000	0.000
119	B	140	ASN	0	-0.023	-0.022	29.346	0.001	0.001	0.000	0.000	0.000	0.000
120	B	141	ALA	0	0.018	0.008	33.026	-0.006	-0.006	0.000	0.000	0.000	0.000
121	B	142	LYS	1	0.921	0.955	32.537	0.114	0.114	0.000	0.000	0.000	0.000
122	B	143	LEU	0	0.057	0.042	37.003	0.001	0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:22:SER)